[gmx-users] How to constraint protein + lipid, to move water into the pore channel

[Maik Goette]

Hi

Generate an index file with make_ndx, put the atoms, you wish to 
restrain (heavy atoms of protein and bilayer e.g.) into one index group.
Then use genpr including the index file and use the index group you made 
for restraints.

Example:

make_ndx -f protein.gro

Screen-Output:
0 System
1 Protein
2 Bilayer

Command:
1|2

Screen-Output:
0 System
1 Protein
2 Bilayer
3 Protein_Bilayer

Command:

3 &! aH*

Screen-Output:
0 System
1 Protein
2 Bilayer
3 Protein_Bilayer
4 Protein_Bilayer_aH*

Command:
q

End Example

You have now written an index file with all heavy atoms of protein and 
Bilayer on position 4. Use this position for restraints in genpr.

Regards


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Chittima Laohpongspaisan wrote:
> Dear All,
> 
> i've just started to rum MD and i'm new gromacs user.
> My system is channel protein in lipid bilayer, now i try to fill waters 
> in the channel pore of protein. plese suggest me how to constraint 
> Protin + Lipid and only move water molecules into the pore (constrain 
> in MD input)
> 
> Best regard,
> JIT
>  
> 
> Chittima Laohpongspaisan
> Advisor: Aj. Supot Hannongbua
> http://192.207.64.1/~chiloo
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